Pre-checkpoint
library(tidyverse)
library(gridExtra)
library(ggplot2)
library(plotly)
library(knitr)

Be sure to include libraries like tidyverse, gridExtra, ggplot2, plotly and knitr.

About EpiCC

Epitope Content Comparison (EpiCC) - A web-based computational method that facilitates pairwise comparison of protein sequences based on immunological property, i.e. T cell epitope content, rather than sequence identity, and evaluated its ability to classify swine influenza A virus (IAV) strain relatedness to estimate cross-protective potential of a vaccine strain for circulating viruses (Gutiérrez et. al, 2017).

Aim

To identify strains that have highest epitope content relatedness to the reference vaccine strain of MHC Class I/II (VACCINE_EPITOPES_CLASSI-NTC8684-ERNA41H-7SOJI/VACCINE_EPITOPES_CLASSII-NTC8682-ERNA41H-1SOJII) across H1N1 Swine IAV whole genome, i.e. a total of 8 protein segments/antigens.

Materials

Input to EpiCC tool: Reference vaccine sequences, MHC ClassI / II versus 72 H1N1 Swine IAV sequences of each protein segment.

Output from EpiCC tool to process and analyze: 8 outfiles for MHC Class I and II respectively.

Methodology/ Working steps

1. Load EpiCC MHC Class I data and clean up unnecessary rows and columns
Quick view of the processed data from one of the protein segments
head(colnames(epicc_data_1_clsI))
## [1] "id"                                                   
## [2] "GB_KY888027-A_SWINE_KANSAS_A01378019_2017-SEGMENT_1"  
## [3] "GB_KY970162-A_SWINE_MICHIGAN_A01259076_2017-SEGMENT_1"
## [4] "GB_MF116355-A_SWINE_KANSAS_A01378027_2017-SEGMENT_1"  
## [5] "GB_MF373215-A_SWINE_IOWA_A01672518_2017-SEGMENT_1"    
## [6] "GB_MF373233-A_SWINE_NEBRASKA_A01672345_2017-SEGMENT_1"
nrow(epicc_data_1_clsI)
## [1] 1
ncol(epicc_data_1_clsI)
## [1] 74
str(epicc_data_1_clsI)
## 'data.frame':    1 obs. of  74 variables:
##  $ id                                                         : chr "VACCINE_EPITOPES_CLASSI-NTC8684-ERNA41H-7SOJI"
##  $ GB_KY888027-A_SWINE_KANSAS_A01378019_2017-SEGMENT_1        : chr "-0.18729"
##  $ GB_KY970162-A_SWINE_MICHIGAN_A01259076_2017-SEGMENT_1      : chr "-0.18784"
##  $ GB_MF116355-A_SWINE_KANSAS_A01378027_2017-SEGMENT_1        : chr "-0.18952"
##  $ GB_MF373215-A_SWINE_IOWA_A01672518_2017-SEGMENT_1          : chr "-0.18745"
##  $ GB_MF373233-A_SWINE_NEBRASKA_A01672345_2017-SEGMENT_1      : chr "-0.18769"
##  $ GB_MF373262-A_SWINE_MINNESOTA_A01672344_2017-SEGMENT_1     : chr "-0.1884"
##  $ GB_MF373280-A_SWINE_NORTH_CAROLINA_A01672011_2017-SEGMENT_1: chr "-0.18762"
##  $ GB_MF373292-A_SWINE_IOWA_A01672342_2017-SEGMENT_1          : chr "-0.18786"
##  $ GB_MF373298-A_SWINE_IOWA_A01672415_2017-SEGMENT_1          : chr "-0.18856"
##  $ GB_MF373304-A_SWINE_ILLINOIS_A01672343_2017-SEGMENT_1      : chr "-0.18856"
##  $ GB_MF521996-A_SWINE_IOWA_A01672824_2017-SEGMENT_1          : chr "-0.18856"
##  $ GB_MF522008-A_SWINE_ILLINOIS_A01932036_2017-SEGMENT_1      : chr "-0.19092"
##  $ GB_MF522032-A_SWINE_MISSOURI_A01672819_2017-SEGMENT_1      : chr "-0.18875"
##  $ GB_MF522038-A_SWINE_MISSOURI_A01932424_2017-SEGMENT_1      : chr "-0.18949"
##  $ GB_MF522050-A_SWINE_INDIANA_A01672825_2017-SEGMENT_1       : chr "-0.18802"
##  $ GB_MF522062-A_SWINE_IOWA_A01932420_2017-SEGMENT_1          : chr "-0.1882"
##  $ GB_MF522068-A_SWINE_NORTH_CAROLINA_A01672751_2017-SEGMENT_1: chr "-0.18675"
##  $ GB_MF664401-A_SWINE_OKLAHOMA_A01672680_2017-SEGMENT_1      : chr "-0.18782"
##  $ GB_MF716915-A_SWINE_OHIO_17TOSU1384_2017-SEGMENT_1         : chr "-0.18966"
##  $ GB_MF716920-A_SWINE_OHIO_17TOSU1386_2017-SEGMENT_1         : chr "-0.18966"
##  $ GB_MF801444-A_SWINE_OHIO_A01354304_2017-SEGMENT_1          : chr "-0.18948"
##  $ GB_MF801452-A_SWINE_ILLINOIS_A02214663_2017-SEGMENT_1      : chr "-0.1882"
##  $ GB_MF801496-A_SWINE_IOWA_A01667089_2017-SEGMENT_1          : chr "-0.18804"
##  $ GB_MF801516-A_SWINE_MINNESOTA_A02214666_2017-SEGMENT_1     : chr "-0.18931"
##  $ GB_MF801522-A_SWINE_MINNESOTA_A01667100_2017-SEGMENT_1     : chr "-0.18782"
##  $ GB_MF801528-A_SWINE_OHIO_A02214229_2017-SEGMENT_1          : chr "-0.18765"
##  $ GB_MF801534-A_SWINE_OHIO_A01354305_2017-SEGMENT_1          : chr "-0.18948"
##  $ GB_MF801554-A_SWINE_IOWA_A01667091_2017-SEGMENT_1          : chr "-0.18641"
##  $ GB_MF801574-A_SWINE_IOWA_A01667088_2017-SEGMENT_1          : chr "-0.18783"
##  $ GB_MF801592-A_SWINE_MICHIGAN_A02214235_2017-SEGMENT_1      : chr "-0.18784"
##  $ GB_MF973284-A_SWINE_OKLAHOMA_A02214419_2017-SEGMENT_1      : chr "-0.18672"
##  $ GB_MF973290-A_SWINE_IOWA_A02214835_2017-SEGMENT_1          : chr "-0.18841"
##  $ GB_MF973314-A_SWINE_MISSOURI_A02214279_2017-SEGMENT_1      : chr "-0.18856"
##  $ GB_MF973344-A_SWINE_MINNESOTA_A02214846_2017-SEGMENT_1     : chr "-0.18819"
##  $ GB_MF973350-A_SWINE_INDIANA_A02214845_2017-SEGMENT_1       : chr "-0.18801"
##  $ GB_MF973356-A_SWINE_IOWA_A02214479_2017-SEGMENT_1          : chr "-0.18838"
##  $ GB_MF973368-A_SWINE_TEXAS_A02214607_2017-SEGMENT_1         : chr "-0.18604"
##  $ GB_MF973374-A_SWINE_NORTH_CAROLINA_A02214775_2017-SEGMENT_1: chr "-0.18911"
##  $ GB_MF973392-A_SWINE_OHIO_A02214848_2017-SEGMENT_1          : chr "-0.18802"
##  $ GB_MG193775-A_SWINE_IOWA_A02215202_2017-SEGMENT_1          : chr "-0.18802"
##  $ GB_MG193787-A_SWINE_MISSOURI_A02216048_2017-SEGMENT_1      : chr "-0.18788"
##  $ GB_MG193793-A_SWINE_ILLINOIS_A02215204_2017-SEGMENT_1      : chr "-0.18948"
##  $ GB_MG193807-A_SWINE_IOWA_A02216046_2017-SEGMENT_1          : chr "-0.18783"
##  $ GB_MG193845-A_SWINE_IOWA_A02216044_2017-SEGMENT_1          : chr "-0.1882"
##  $ GB_MG193857-A_SWINE_IOWA_A02216456_2017-SEGMENT_1          : chr "-0.18819"
##  $ GB_MG193869-A_SWINE_OHIO_A02215367_2017-SEGMENT_1          : chr "-0.18765"
##  $ GB_MG193891-A_SWINE_IOWA_A02215041_2017-SEGMENT_1          : chr "-0.18891"
##  $ GB_MG193903-A_SWINE_IOWA_A02215038_2017-SEGMENT_1          : chr "-0.18782"
##  $ GB_MG521000-A_SWINE_ILLINOIS_A02218178_2017-SEGMENT_1      : chr "-0.18783"
##  $ GB_MG521006-A_SWINE_IOWA_A02217313_2017-SEGMENT_1          : chr "-0.18858"
##  $ GB_MG521024-A_SWINE_NEBRASKA_A02216645_2017-SEGMENT_1      : chr "-0.1871"
##  $ GB_MG521030-A_SWINE_INDIANA_A02216644_2017-SEGMENT_1       : chr "-0.18765"
##  $ GB_MG521042-A_SWINE_OHIO_A02216472_2017-SEGMENT_1          : chr "-0.18874"
##  $ GB_MG521048-A_SWINE_IOWA_A02217282_2017-SEGMENT_1          : chr "-0.18841"
##  $ GB_MG521108-A_SWINE_INDIANA_A02218180_2017-SEGMENT_1       : chr "-0.18948"
##  $ GB_MG521114-A_SWINE_WISCONSIN_A01104100_2017-SEGMENT_1     : chr "-0.18948"
##  $ GB_MG650642-A_SWINE_IOWA_A02218171_2017-SEGMENT_1          : chr "-0.1882"
##  $ GB_MG662553-A_SWINE_IOWA_A02218755_2017-SEGMENT_1          : chr "-0.18799"
##  $ GB_MG662571-A_SWINE_NORTH_CAROLINA_A01785281_2017-SEGMENT_1: chr "-0.18783"
##  $ GB_MG662601-A_SWINE_MISSOURI_A02218334_2017-SEGMENT_1      : chr "-0.18856"
##  $ GB_MG662637-A_SWINE_IOWA_A01104104_2017-SEGMENT_1          : chr "-0.1871"
##  $ GB_MG662657-A_SWINE_IOWA_A02218750_2017-SEGMENT_1          : chr "-0.18875"
##  $ GB_MG662677-A_SWINE_ARKANSAS_A02218161_2017-SEGMENT_1      : chr "-0.18893"
##  $ GB_MG784562-A_SWINE_IOWA_A02221505_2017-SEGMENT_1          : chr "-0.18784"
##  $ GB_MG784568-A_SWINE_NEBRASKA_A02219793_2017-SEGMENT_1      : chr "-0.18969"
##  $ GB_MG784580-A_SWINE_IOWA_A02221508_2017-SEGMENT_1          : chr "-0.18785"
##  $ GB_MG784592-A_SWINE_IOWA_A02221506_2017-SEGMENT_1          : chr "-0.18801"
##  $ GB_MG784616-A_SWINE_OHIO_A02219547_2017-SEGMENT_1          : chr "-0.18909"
##  $ GB_MG784628-A_SWINE_NORTH_CAROLINA_A01785282_2017-SEGMENT_1: chr "-0.18856"
##  $ GB_MG784646-A_SWINE_ILLINOIS_A02219783_2017-SEGMENT_1      : chr "-0.18837"
##  $ GB_MG835451-A_SWINE_KANSAS_A01378037_2017-SEGMENT_1        : chr "-0.18824"
##  $ GB_MG912578-A_SWINE_KANSAS_A01378038_2017-SEGMENT_1        : chr "-0.18732"
##  $ VACCINE_EPITOPES_CLASSI-NTC8684-ERNA41H-7SOJI              : chr "0.05574"
2. Transform data from wide form to long form, perform sorting and extracting top 10 EpiCC score from each protein
Showing a working example from one of the protein segments: PB2
epicc_data_1_clsI_long <- epicc_data_1_clsI %>% 
  gather(key = strains, value = PB2_score, 
         `GB_KY888027-A_SWINE_KANSAS_A01378019_2017-SEGMENT_1`:`VACCINE_EPITOPES_CLASSI-NTC8684-ERNA41H-7SOJI`) %>% 
  select(strains,PB2_score) %>% mutate(header = strains) %>% 
  separate(header, into = c("ID", "Sequence", "Segment"), sep = "-", extra = "merge")
epicc_data_1_clsI_long$PB2_score <- as.numeric(epicc_data_1_clsI_long$PB2_score)
epicc_data_1_clsI_sort <- epicc_data_1_clsI_long %>% filter(!Sequence == "NTC8684") %>%
  arrange(Sequence) %>% arrange(desc(PB2_score))
epicc_data_1_clsI_top10 <- head(epicc_data_1_clsI_sort, 10)
epicc_data_1_clsI_top10 <- epicc_data_1_clsI_top10 %>% select(Sequence, Segment)
epicc_data_1_clsI_top10
##                                 Sequence   Segment
## 1           A_SWINE_TEXAS_A02214607_2017 SEGMENT_1
## 2            A_SWINE_IOWA_A01667091_2017 SEGMENT_1
## 3        A_SWINE_OKLAHOMA_A02214419_2017 SEGMENT_1
## 4  A_SWINE_NORTH_CAROLINA_A01672751_2017 SEGMENT_1
## 5            A_SWINE_IOWA_A01104104_2017 SEGMENT_1
## 6        A_SWINE_NEBRASKA_A02216645_2017 SEGMENT_1
## 7          A_SWINE_KANSAS_A01378019_2017 SEGMENT_1
## 8          A_SWINE_KANSAS_A01378038_2017 SEGMENT_1
## 9            A_SWINE_IOWA_A01672518_2017 SEGMENT_1
## 10 A_SWINE_NORTH_CAROLINA_A01672011_2017 SEGMENT_1
2a. Exploratory analysis of H1N1 Swine IAV dataset
3. Combine top 10 EpiCC score from each protein
MHC Class I top 10 data preview
head(epicc_data_clsI_top10_all)
##                                Sequence   Segment
## 1          A_SWINE_TEXAS_A02214607_2017 SEGMENT_1
## 2           A_SWINE_IOWA_A01667091_2017 SEGMENT_1
## 3       A_SWINE_OKLAHOMA_A02214419_2017 SEGMENT_1
## 4 A_SWINE_NORTH_CAROLINA_A01672751_2017 SEGMENT_1
## 5           A_SWINE_IOWA_A01104104_2017 SEGMENT_1
## 6       A_SWINE_NEBRASKA_A02216645_2017 SEGMENT_1
tail(epicc_data_clsI_top10_all)
##                            Sequence   Segment
## 75 A_SWINE_MINNESOTA_A02214666_2017 SEGMENT_8
## 76    A_SWINE_KANSAS_A01378027_2017 SEGMENT_8
## 77      A_SWINE_IOWA_A02215041_2017 SEGMENT_8
## 78      A_SWINE_IOWA_A02216456_2017 SEGMENT_8
## 79      A_SWINE_OHIO_A02219547_2017 SEGMENT_8
## 80   A_SWINE_INDIANA_A02216644_2017 SEGMENT_8
unique(epicc_data_clsI_top10_all$Sequence)
##  [1] "A_SWINE_TEXAS_A02214607_2017"         
##  [2] "A_SWINE_IOWA_A01667091_2017"          
##  [3] "A_SWINE_OKLAHOMA_A02214419_2017"      
##  [4] "A_SWINE_NORTH_CAROLINA_A01672751_2017"
##  [5] "A_SWINE_IOWA_A01104104_2017"          
##  [6] "A_SWINE_NEBRASKA_A02216645_2017"      
##  [7] "A_SWINE_KANSAS_A01378019_2017"        
##  [8] "A_SWINE_KANSAS_A01378038_2017"        
##  [9] "A_SWINE_IOWA_A01672518_2017"          
## [10] "A_SWINE_NORTH_CAROLINA_A01672011_2017"
## [11] "A_SWINE_NEBRASKA_A02219793_2017"      
## [12] "A_SWINE_INDIANA_A01672825_2017"       
## [13] "A_SWINE_ILLINOIS_A02218178_2017"      
## [14] "A_SWINE_IOWA_A02216046_2017"          
## [15] "A_SWINE_ILLINOIS_A01932036_2017"      
## [16] "A_SWINE_ILLINOIS_A01672343_2017"      
## [17] "A_SWINE_ILLINOIS_A02214663_2017"      
## [18] "A_SWINE_IOWA_A02214835_2017"          
## [19] "A_SWINE_MINNESOTA_A02214666_2017"     
## [20] "A_SWINE_IOWA_A02215202_2017"          
## [21] "A_SWINE_KANSAS_A01378027_2017"        
## [22] "A_SWINE_IOWA_A01667089_2017"          
## [23] "A_SWINE_IOWA_A02221505_2017"          
## [24] "A_SWINE_IOWA_A02217282_2017"          
## [25] "A_SWINE_IOWA_A02215038_2017"          
## [26] "A_SWINE_ILLINOIS_A02219783_2017"      
## [27] "A_SWINE_OHIO_17TOSU1384_2017"         
## [28] "A_SWINE_OHIO_17TOSU1386_2017"         
## [29] "A_SWINE_OHIO_A01354304_2017"          
## [30] "A_SWINE_OHIO_A01354305_2017"          
## [31] "A_SWINE_OKLAHOMA_A01672680_2017"      
## [32] "A_SWINE_MISSOURI_A01932424_2017"      
## [33] "A_SWINE_NORTH_CAROLINA_A01785281_2017"
## [34] "A_SWINE_KANSAS_A01378037_2017"        
## [35] "A_SWINE_IOWA_A02215041_2017"          
## [36] "A_SWINE_IOWA_A02216456_2017"          
## [37] "A_SWINE_OHIO_A02219547_2017"          
## [38] "A_SWINE_INDIANA_A02216644_2017"
unique(epicc_data_clsI_top10_all$Segment)
## [1] "SEGMENT_1" "SEGMENT_2" "SEGMENT_3" "SEGMENT_4" "SEGMENT_5" "SEGMENT_6"
## [7] "SEGMENT_7" "SEGMENT_8"
4. Identify the most occuring strains, i.e. strains with high frequency
max(most_occurence_strain_clsI$count)
## [1] 5
most_occurence_strain_clsI
## # A tibble: 12 x 2
##                           Sequence count
##                              <chr> <int>
##  1     A_SWINE_IOWA_A01672518_2017     5
##  2     A_SWINE_IOWA_A02215202_2017     5
##  3     A_SWINE_IOWA_A02221505_2017     5
##  4     A_SWINE_IOWA_A01104104_2017     4
##  5     A_SWINE_IOWA_A01667091_2017     4
##  6     A_SWINE_IOWA_A02214835_2017     4
##  7     A_SWINE_IOWA_A02215038_2017     4
##  8   A_SWINE_KANSAS_A01378027_2017     4
##  9    A_SWINE_TEXAS_A02214607_2017     4
## 10 A_SWINE_ILLINOIS_A01932036_2017     3
## 11   A_SWINE_KANSAS_A01378038_2017     3
## 12 A_SWINE_NEBRASKA_A02216645_2017     3

Maximum frequency = 5 out of 8 (if the EpiCC score of a strain remain in the top 10 list of all proteins, then it will have frequency of 8). In this case, since the maximum frequency is only 5, this means that these strains are only found in the top 10 list of 5 proteins. Here, we considered strains that of frequency between 3 - 5.

5. Repeat steps 1 - 4 for MHC Class II data
MHC Class II top 10 data preview
head(epicc_data_clsII_top10_all)
##                          Sequence   Segment
## 1   A_SWINE_KANSAS_A01378019_2017 SEGMENT_1
## 2 A_SWINE_MISSOURI_A01932424_2017 SEGMENT_1
## 3   A_SWINE_KANSAS_A01378027_2017 SEGMENT_1
## 4     A_SWINE_OHIO_A02219547_2017 SEGMENT_1
## 5 A_SWINE_NEBRASKA_A02219793_2017 SEGMENT_1
## 6 A_SWINE_OKLAHOMA_A02214419_2017 SEGMENT_1
tail(epicc_data_clsII_top10_all)
##                                 Sequence   Segment
## 75         A_SWINE_KANSAS_A01378027_2017 SEGMENT_8
## 76       A_SWINE_NEBRASKA_A02219793_2017 SEGMENT_8
## 77 A_SWINE_NORTH_CAROLINA_A01785281_2017 SEGMENT_8
## 78         A_SWINE_KANSAS_A01378019_2017 SEGMENT_8
## 79       A_SWINE_MISSOURI_A02216048_2017 SEGMENT_8
## 80           A_SWINE_IOWA_A02221506_2017 SEGMENT_8
unique(epicc_data_clsII_top10_all$Sequence)
##  [1] "A_SWINE_KANSAS_A01378019_2017"        
##  [2] "A_SWINE_MISSOURI_A01932424_2017"      
##  [3] "A_SWINE_KANSAS_A01378027_2017"        
##  [4] "A_SWINE_OHIO_A02219547_2017"          
##  [5] "A_SWINE_NEBRASKA_A02219793_2017"      
##  [6] "A_SWINE_OKLAHOMA_A02214419_2017"      
##  [7] "A_SWINE_IOWA_A01672342_2017"          
##  [8] "A_SWINE_KANSAS_A01378038_2017"        
##  [9] "A_SWINE_ILLINOIS_A02218178_2017"      
## [10] "A_SWINE_IOWA_A01667088_2017"          
## [11] "A_SWINE_NORTH_CAROLINA_A01672751_2017"
## [12] "A_SWINE_NORTH_CAROLINA_A01785281_2017"
## [13] "A_SWINE_IOWA_A01672824_2017"          
## [14] "A_SWINE_IOWA_A02214479_2017"          
## [15] "A_SWINE_MISSOURI_A02214279_2017"      
## [16] "A_SWINE_NORTH_CAROLINA_A01785282_2017"
## [17] "A_SWINE_ILLINOIS_A01932036_2017"      
## [18] "A_SWINE_MISSOURI_A02216048_2017"      
## [19] "A_SWINE_IOWA_A02221508_2017"          
## [20] "A_SWINE_OKLAHOMA_A01672680_2017"      
## [21] "A_SWINE_NORTH_CAROLINA_A01672011_2017"
## [22] "A_SWINE_IOWA_A02215038_2017"          
## [23] "A_SWINE_ARKANSAS_A02218161_2017"      
## [24] "A_SWINE_TEXAS_A02214607_2017"         
## [25] "A_SWINE_IOWA_A02215202_2017"          
## [26] "A_SWINE_IOWA_A01104104_2017"          
## [27] "A_SWINE_IOWA_A02214835_2017"          
## [28] "A_SWINE_NEBRASKA_A02216645_2017"      
## [29] "A_SWINE_IOWA_A01672518_2017"          
## [30] "A_SWINE_IOWA_A02221505_2017"          
## [31] "A_SWINE_IOWA_A02217282_2017"          
## [32] "A_SWINE_KANSAS_A01378037_2017"        
## [33] "A_SWINE_MINNESOTA_A02214666_2017"     
## [34] "A_SWINE_NEBRASKA_A01672345_2017"      
## [35] "A_SWINE_ILLINOIS_A02219783_2017"      
## [36] "A_SWINE_IOWA_A02221506_2017"
unique(epicc_data_clsII_top10_all$Segment)
## [1] "SEGMENT_1" "SEGMENT_2" "SEGMENT_3" "SEGMENT_4" "SEGMENT_5" "SEGMENT_6"
## [7] "SEGMENT_7" "SEGMENT_8"
max(most_occurence_strain_clsII$count)
## [1] 7
most_occurence_strain_clsII
## # A tibble: 14 x 2
##                                 Sequence count
##                                    <chr> <int>
##  1         A_SWINE_KANSAS_A01378027_2017     7
##  2       A_SWINE_ILLINOIS_A01932036_2017     6
##  3           A_SWINE_IOWA_A02215038_2017     4
##  4         A_SWINE_KANSAS_A01378038_2017     4
##  5 A_SWINE_NORTH_CAROLINA_A01785281_2017     4
##  6       A_SWINE_OKLAHOMA_A02214419_2017     4
##  7           A_SWINE_IOWA_A01104104_2017     3
##  8           A_SWINE_IOWA_A01672518_2017     3
##  9           A_SWINE_IOWA_A02215202_2017     3
## 10         A_SWINE_KANSAS_A01378019_2017     3
## 11         A_SWINE_KANSAS_A01378037_2017     3
## 12       A_SWINE_MISSOURI_A02216048_2017     3
## 13       A_SWINE_NEBRASKA_A02216645_2017     3
## 14       A_SWINE_OKLAHOMA_A01672680_2017     3

Maximum frequency = 7 out of 8. Same selection criteria as Class I data, we considered strains that of frequency between 3 - 5.

6. To plot the frequency of MHC Class I/II top 10 strains from all 8 proteins

This figure shows strains that are found in the top 10 list of every proteins and their frequencies were counted. This is to identify strains that are constantly having high EpiCC score across the whole genome.

Upper panel shows there are 3 strains have a frequency of 5; 6 strains of frequency 4; 3 strains of frequency 3; 6 strains of frequency 2 and 20 strains of frequency 1.

Lower panel shows there is 1 strain has frequency of 7 and 6, respectively; 4 strains of frequency 4; 8 strains of frequency 3; 5 strains of frequency 2 and 17 strains of frequency 1.

7. Identify strains that are common in both Class I and Class II

Result

common
## # A tibble: 8 x 2
##                          Sequence count
##                             <chr> <int>
## 1   A_SWINE_KANSAS_A01378027_2017     7
## 2 A_SWINE_ILLINOIS_A01932036_2017     6
## 3     A_SWINE_IOWA_A02215038_2017     4
## 4   A_SWINE_KANSAS_A01378038_2017     4
## 5     A_SWINE_IOWA_A01104104_2017     3
## 6     A_SWINE_IOWA_A01672518_2017     3
## 7     A_SWINE_IOWA_A02215202_2017     3
## 8 A_SWINE_NEBRASKA_A02216645_2017     3

There are 8 Swine IAV found in both Class I and Class II top EpiCC score list. This means 8 of these strains are having relatively high epitope content to the reference vaccine strain compared to other H1N1 Swine IAV sequences.